Tuesday, April 14, 2015

Clinical Research Informatics

American Medical Informatics Association

Canadian Primary Care Sentinel Surveillance Network:

IRB Class Model

Clinical research informatics: a conceptual perspective


Clinical research informatics is the rapidly evolving sub-discipline within biomedical informatics that focuses on developing new informatics theories, tools, and solutions to accelerate the full translational continuum: basic research to clinical trials (T1), clinical trials to academic health center practice (T2), diffusion and implementation to community practice (T3), and ‘real world’ outcomes (T4). We present a conceptual model based on an informatics-enabled clinical research workflow, integration across heterogeneous data sources, and core informatics tools and platforms. We use this conceptual model to highlight 18 new articles in the JAMIA special issue on clinical research informatics.
Keywords: Clinical research informatics, clinical and translational research, visualization of data and knowledge, knowledge representations, methods for integration of information from disparate sources, data models, data exchange, knowledge bases, knowledge acquisition, knowledge acquisition and knowledge management

Saturday, March 14, 2015

Kurzweil Accelerating Intelligence weekly newsletter

I always look forward to Fridays when I get to read the Kuzweil Accelerating Intelligence newsletter. It has got to be one of the seven wonders of the world. The future is always HERE  NOW.

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KurzweilAI | Accelerating Intelligence. Newsletter
Friday March 13, 2015

Turning smartphones into personal, real-time pollution-location monitors
March 13, 2015

A small pollution sensor was used to measure their black carbon level continuously, combined with an Android smartphone with CalFit software for recording GPS information on user location (credit: Mark J. Nieuwenhuijsen et al./Environmental Science & Technology)Scientists reporting in the ACS journal Environmental Science & Technology have used smartphone and sensing technology to better pinpoint times and locations of the worst air pollution, which is associated with respiratory and cardiovascular problems. Most such studies create a picture of exposure based on air pollution levels outside people’s homes. This approach ignores big differences in …more…

Out of their minds: a thrilling ride that adapts to riders’ brain activity
March 13, 2015

(credit: Horizon Digital Economy Research)A new ride called Neurosis, based on research from The University of Nottingham, adapts the experience to the rider’s own brain activity. Its world premiere will be at the FutureFest festival taking place in London this weekend. It draws on research being conducted by performance artist/professor Brendan Walker, a principal research fellow in the University’s School of … more…

Chameleon-like artificial ‘skin’ shifts color on demand
March 13, 2015

Developed by engineers from the University of California at Berkeley, this chameleon-like artificial "skin" changes color as a minute amount of force is applied. (credit: The Optical Society/OSA)Engineers from the University of California at Berkeley have created an incredibly thin, chameleon-like material that can be made to change color on demand by simply flexing it with a tiny amount of force. This new material-of-many-colors offers intriguing possibilities for an entirely new class of display technologies, color-shifting camouflage, and sensors that can detect … more…

Vast underground ocean discovered on Jupiter’s largest moon
March 13, 2015

This is an illustration of the interior of Jupiter's largest moon, Ganymede. It is based on theoretical models, in-situ observations by NASA's Galileo orbiter, and Hubble Space Telescope observations of the moon's aurorae, which allows for a probe of the moon's interior. The cake-layering of the moon shows that ices and a saline ocean dominate the outer layers. A denser rock mantle lies deeper in the moon, and finally an iron core beneath that. (credit: NASA, ESA and A. Feild/STScI)
"A deep ocean under the icy crust of Ganymede opens up further exciting possibilities for life beyond Earth” --- NASA
NASA’s Hubble Space Telescope has the best evidence yet for an underground saltwater ocean on Ganymede, Jupiter’s largest moon. The subterranean ocean is thought to have more water than all the water on Earth’s surface. Identifying liquid water is crucial in the search for habitable worlds beyond Earth and for the search of life as … more…

A ‘visual Turing test’ of computer ‘understanding’ of images
March 12, 2015

Athens, Baltimore, Hong Kong, Miami. What are those people doing? A new evaluation method measures a computer’s ability to decipher movements, relationships, and implied intent from images by asking questions (Credit: Brown University)Researchers from Brown and Johns Hopkins universities have come up with a new way to evaluate how well computers can “understand” the relationships or implied activities between objects in photographs, videos, and other images, not just recognize objects — a “visual Turing test,” as they describe it. Traditional computer-vision benchmarks tend to measure an algorithm’s … more…

The corrugated galaxy — Milky Way may be much larger than previously estimated
March 12, 2015

The Milky Way galaxy is at least 50 percent larger than is commonly estimated, according to new findings that reveal that the galactic disk is contoured into several concentric ripples. (Credit: Rensselaer Polytechnic Institute)The Milky Way galaxy is at least 50 percent larger than is commonly estimated, according to new findings that reveal that the galactic disk is contoured into several concentric ripples. The research, conducted by an international team led by Rensselaer Polytechnic Institute Professor Heidi Jo Newberg, revisits astronomical data from the Sloan Digital Sky Survey … more…

A ’3D printer’ for customized small molecules such as drugs
March 12, 2015

3D Printer for Small Molecules1Howard Hughes Medical Institute scientists have developed a simpler way to synthesize small molecules, eliminating a major bottleneck in creating new medicines. As the scientists note in the March 13, 2015, issue of the journal Science, “small-molecule syntheses typically employ strategies and purification methods that are highly customized for each target, thus requiring automation solutions to … more…

Bio-inspired eye stabilizes robot’s flight, replaces inertial navigation system
March 11, 2015

The BeeRotor robot, equipped with an eye inspired by that of insects (credit: © Expert & Ruffier (ISM, CNRS/AMU))Biorobotics researchers have developed the first aerial robot able to fly over uneven terrain that is stabilized visually without an accelerometer. Called BeeRotor, it adjusts its speed and avoids obstacles thanks to optic flow sensors inspired by insect vision. It can fly along a tunnel with uneven, moving walls without measuring either speed or altitude. … more…

Silk may be the new ‘green’ ultra-high-capacity material for batteries
March 11, 2015

Silk is graphetized (left) to create porous nitrogen-doped carbon nanosheets as an improved ultra-high-capacity material for battery anodes and supercapacitors (credit: Jianhau Hou et al./ACS Nano)Scientists at Beijing Institute of Technology have developed a new “green” method to boost the performance of widely used lithium-ion (Li-ion) batteries, using a material derived from silk. Currently, graphite (a form of  carbon found in “lead” pencils) is used in Li-ion energy storage devices, including batteries and supercapacitors. Chuanbao Cao and colleagues found a … more…

‘Heart on a chip’ reduces time and cost in drug testing for safety and efficacy
March 10, 2015

The “heart-on-a-chip” developed at UC Berkeley houses human heart tissue derived from adult stem cells. The system could one day replace animal models for drug safety screening. (credit: Anurag Mathur, Healy Lab)
Replaces animal models, which have a high failure rate in predicting human reactions to new drugs
A UC Berkeley research team led by bioengineering professor Kevin Healy has developed a network of pulsating cardiac muscle cells that models human heart tissue. They have also demonstrated the viability of this system as a drug-screening tool by testing it with cardiovascular medications. This “organ-on-a-chip,” housed in an inch-long silicone (a rubberlike material) device, … more…

Drugs that dramatically increase healthy lifespan discovered by Scripps Research, Mayo Clinic
March 10, 2015

Sprycel (credit: Bristol-Myers Squibb)A research team from The Scripps Research Institute (TSRI), Mayo Clinic and other institutions has identified a new class of drugs that in animal models dramatically slows the aging process, alleviating symptoms of frailty, improving cardiac function, and extending a healthy lifespan. They found two drugs — the cancer drug dasatinib (sold under the trade name Sprycel) and quercetin, …more…

Future farming to be based on robots and big data
March 9, 2015

QUT's AgBot II (credit: QUT)The farm of the future will involve multiple lightweight, small, autonomous, energy-efficient machines (AgBots) operating collectively to weed, fertilize and control pest and diseases, while collecting vasts amount of data to enable better management decision making,” according to Queensland University of Technology (QUT) robotics Professor Tristan Perez. “We are starting to see automation in agriculture for … more…

First detailed microscopy evidence of ‘nanobacteria’ at the lower size limit of life
March 9, 2015

This cryo-electron tomography image reveals the internal structure of an ultra-small bacteria cell like never before. The cell has a very dense interior compartment and a complex cell wall. The darker spots at each end of the cell are most likely ribosomes. The image was obtained from a 3-D reconstruction. The scale bar is 100 nanometers. (Credit: Berkeley Lab)Scientists have captured the first detailed microscopy images of ultra-small bacteria believed to be about as small as life can get. The existence of ultra-small bacteria (aka “nanobacteria” or “nannobacteria”) has been debated for two decades, but there hasn’t been a comprehensive electron microscopy and DNA-based description of the microbes until now. They are about … more…

Hidden toxins found in ‘green,’ ‘all-natural,’ and ‘organic’ products
March 8, 2015

(credit: iStock)
Fewer than three percent of volatile ingredients identified
A University of Melbourne researcher has found that common consumer products, including those marketed as “green,” “all-natural,” “non-toxic,” and “organic,” emit a range of compounds that could harm human health and air quality. But most of these ingredients are not disclosed to the public. Prof. Anne Steinemann* investigated and compared volatile organic compounds (VOCs) emitted … more…



Dates: Mar 14 – 15, 2015
Location: London, England



Dates: Mar 22 – 26, 2015
Location: Los Angeles, CA


8th AGI conferenceAGI-15 @ Berlin

Dates: Jul 22 – 25, 2015
Location: Berlin, Germany


tedmed_logo_retinaTEDMED 2015

Dates: Nov 18 – 20, 2015
Location: Palm Springs, CA


Visit KurzweilAI.net

KurzweilAINetwork, Inc. 733 Turnpike Street Suite 193 North Andover, MA 01845 USA.

Wednesday, February 4, 2015

Personal Health Record Push to Apps

I sometimes follow the HL7 group on Personal Health Records. I received this email from a member of the group. I find it interesting that pushing medical records to a personal health record is becoming better:

NBB4C makes it easier for providers to share health information with their patients so that their patients can do what they want with it.

February 2015

Clearing the Way for Patients to Get Access to their Data
National Association for Trusted Exchange Unveils New Trust Community for Exchange with Consumers
WASHINGTON, D.C. (February 3, 2015) – The National Association for Trusted Exchange (NATE) today kicked off its new NATE Blue Button for Consumers (NBB4C) Trust Bundle at the 2015 ONC Annual Meeting with a surprise display of interoperability in patient-mediated exchange.  Shortly after NATE’s announcement, Greg Meyer, Director, Distinguished Engineer, Cerner Corporation, demonstrated how a provider using a Cerner electronic medical record (EMR) can simply push a patient record to the patient's personal health record (PHR), in this case to the Humetrix iBlueButton app running on the patient's smartphone.

The new NBB4C Trust Bundle helps relying parties to identify consumer facing applications (CFAs) that meet or exceed criteria considered to be the most important characteristics of a trustworthy steward of consumer health information, while still enabling patients to benefit from the value of having access to their health information.  Participation in the trust bundle will facilitate secure exchange of health information from provider-controlled applications to consumer-controlled applications such as PHRs using Direct secure messaging protocols.

“Thank you to my colleagues at Cerner and Humetrix for helping NATE demonstrate the capabilities of the new NATE Blue Button for Consumers Trust Bundle at the ONC Annual Meeting.  Greg’s demonstration today shows that the NBB4C is ready now to enable real world exchange between provider-facing applications and consumer-facing applications, empowering the consumer to get access to their data,” said NATE’s CEO Aaron Seib.  “Our industry achieved a major milestone today.  We studied the issues around securely sharing information from providers to patients and together we took a leap of faith.  Consumers across the country will now have more control over their care.  NBB4C gets the information flowing to where it should be: in the hands of the patient.  I look forward to the day when patients across the nation routinely download their health information into a consumer-facing application of their choice and use it to improve their lives and the lives of those they love.”

The NBB4C Trust Bundle is the result of the next generation of NATE’s ongoing PHR Ignite Project and incorporates lessons learned from NATE’s administration of the Blue Button Consumer Trust Bundles.  Over the past year, NATE and a task group made up of thought leaders in the patient-mediated exchange space worked together to develop a set of criteria and expectations that balances what is a ‘must have’ for today and what can wait until tomorrow, what is practical as a starting point and what is a showstopper that would kill consumer engagement if introduced.  In November 2014, NATE crowd sourced the trust framework, calling for and receiving comments from across the industry.  In January 2015, the NATE Board of Directors approved the workgroup’s recommendation for release into production.

“The NBB4C establishes a practical framework that will enable patients to securely exchange health information with their providers without burdening the patient with unnecessary steps to obtain their data and share it with whomever they choose,” said MaryAnne Sterling, Consumer Ombudsman for the NATE Board of Directors.  “As a long time caregiver for my aging parents, this work is important to all of us who manage healthcare on behalf of others.  I have confidence that applications participating in the NBB4C will meet or exceed my expectation that my family’s health information will be confidential and secure.”
Interested CFAs may begin onboarding to the NBB4C Trust Bundle now at http://nate-trust.org/trustbundles.  Stakeholders interested in participating in the next phase of NATE’s work in consumer-mediated exchange should consider NATE membership or subscribe to news from NATE’s PHR Community.
# # #
NBB4C makes it easier for providers to share health information with their patients so that their patients can do what they want with it.
About National Association for Trusted Exchange
The National Association for Trusted Exchange (NATE) brings the expertise of its membership and other stakeholders together to find common solutions that optimize the appropriate exchange of health information for greater gains in adoption and outcomes. Emerging from the Western States Consortium, a pilot project supported by the Office of the National Coordinator for Health Information Technology (ONC), NATE was established as a not-for-profit organization in May 2013. Consistent with NATE’s mission to address the legal, policy, and technical barriers that inhibit health information exchange between entities within a state and across states, NATE leads and participates in a number of ongoing and emerging projects in the HIE domain. NATE has been operating its own Trust Bundles in production since November 2012 and recently took over administration of the Blue Button Consumer Trust Bundles.  Working with a broad set of stakeholders through multiple task forces, crowdsourcing and a call for public comment, NATE is proud to make available the first release of NATE's Blue Button for Consumers (NBB4C) Trust Bundle beginning in 2015.

About Cerner 

Cerner’s health information technologies connect people, information and systems at more than 18,000 facilities worldwide. Recognized for innovation, Cerner solutions assist clinicians in making care decisions and enable organizations to manage the health of populations. The company also offers an integrated clinical and financial system to help health care organizations manage revenue, as well as a wide range of services to support clients’ clinical, financial and operational needs. Cerner’s mission is to contribute to the improvement of health care delivery and the health of communities. Nasdaq: CERN. For more information about Cerner, visit cerner.com, read our blog at cerner.com/blog, connect with us on Twitter at twitter.com/cerner and on Facebook at facebook.com/cerner.
As of February 2, 2015, Cerner Corporation acquired Siemens Health Services.  Certain trademarks, service marks and logos set forth herein are property of Cerner Corporation and/or its subsidiaries. All other non-Cerner marks are the property of their respective owners.
About Humetrix
Humetrix has pioneered the development of innovative consumer-centered IT solutions over the past 15 years, which have been deployed around the world.  The company’s award winning Blue Button enabled apps are the mobile embodiment of the U.S. Federal government Blue Button initiative available to more than 150 million Americans. Humetrix’s HHS award winning emergency and disaster preparedness mobile apps are now being advocated by EMS agencies across the US and were demonstrated at the White House Innovation for Disaster Response and Recovery Demo Day last summer. For more information, visit www.ibluebutton.com and www.humetrix.com

Copyright © 2015 National Association for Trusted Exchange. All rights reserved.
Contact email: meryt.mcgindley@nate-trust.org

You are receiving this message because you have an interest in health information exchange.

Tuesday, January 27, 2015

Personalised Medicine and/or Personalised Health Information Services

I came across a website and eHealth service recently called Medivizor. Seems like I have had the wrong idea about what "personalised medicine" means. I needed to enter it as a search term in Pubmed and discovered 932 articles that had nothing to do with my idea of it. That is, my idea was more in line with the health information services provided by Medivizor. The articles I found in Pubmed were more like "personalized genomics or pharmaceuticals". For example, this article: "Metabolomics as a tool for drug discovery and personalised medicine. A review."

While there may be nothing wrong with that, especially if they want to use genomics to replace parts in me, my idea had more to do with the kinds of health information one should be getting through a personal health record (ePHR), depending on one's own unique state of health. But if I do a Pubmed search on "personalised medicine and personal health records", I get almost exactly what I am thinking about (but only 6 articles). The first article is called:

Wang HQ, Li JS, Zhang YF, Suzuki M, Araki K.
Artif Intell Med. 2013 Jun;58(2):81-9. doi: 10.1016/j.artmed.2013.02.005. Epub 2013 Mar 5.
People search the net for health information and Google is a vast resource. It is better to narrow the scope and only get the health information related to one's personal conditions or searching - be they chronic or not - and to make sure that information is trusted. The Optimal Aging Portal is one such service, but at the current time, that information isn't being personalised or fed into individual ePHRs. All is not lost: patients do have their family doctor for personalised medical attention. End of story.

Getting that trusted health information, if it isn't directly from your family doctor, is a work of monumental scientific promise. A recent overview article that caught the interest of the health informatics community is found here: "Stop Googling your health questions. Use these sites instead":
That's a lot of knowledge translation to get healthcare consumers to wise up about the health information they are seeking.

The best idea would be if the there is a health informatics professional(s) in the family health team who can work in consultation with the family doctor so that personalized and trusted health information most relevant for them is getting to them through the ePHR. Can't leave it all up to AI and algorithms, but who knows?

Saturday, November 22, 2014

Wednesday, November 12, 2014

Mindfulness Based Stress Reduction: Learn online or from an actual human teacher?

Around 40 years ago, I studied with one of the greatest Tai Chi Ch'uan masters of the last century,  Cheng Man-ch'ing. The thing is, I never studied with him in person. I had his book, which was illustrated with photographs of him doing the movements; The Golden Pheasant Stands On One Leg, Grasp The Sparrow's Tail, The Crane Spreads It's Wings, Step Forward to the Seven Stars of the Dipper, Snake Creeps Down, The Fairy Weaving at the Shuttle, etc. By looking in a mirror I thought I was able to string together a series of movements. Wrong!  I was only twisting and hurting my back and other places doing the exercises. Seven years later I met a Tai Chi Ch'uan teacher and the realization that this ancient art can only be learned by being passed down from teacher to student.

That was before the age of the ubiquitous computer. Nowadays I can watch Tai Chi instructional videos on Youtube all day. I can even switch to other physical activities and watch instructional videos about how to improve my tennis forehand. Ultimately though, I need to really practice the actual art or sport in order to derive any benefit. To really improve at all I should practice with a teacher or coach. There comes a time when we do need to meet human instructors in person to really learn. This is especially true for some of the physiotherapy exercises you can watch on Youtube because I think it is be better to have a physiotherapist prescribe the exercises.  I do know a Tai Chi practitioner who learned the Chan form of Tai Chi by watching videos he had borrowed. He was exceptional in that he already knew and practiced many other of the Tai Chi forms. And this brings me to Mindfulness Based Stress Reduction (MBSR) learning online.

Before I comment about what it is like to learn MBSR online, let's look at the movie the Matrix. If you have seen the movie, you know that when Neo was hooked-up into the Matrix, he learned and later mastered Kung-fu, in addition to several other martial arts, at the speed of digital data transfer and integration into programming. That would be the epitome of hooked-up online learning. The next computerized training ground, that is not science fiction, maybe be Oculus Rift, a newer virtual reality headset that brings into visual perception an immersion experience of three dimensions.

It wasn't that long ago, virtually since the dawn of the WWW, when educators had to face the dilemma of evaluating whether or not one can learn just as well by studying online as one could in a classroom. We can see now how technology, even in science fiction, has grown exponentially to make online learning as common as the air that we breath. That is why before MOOCs there were online courses where you could even get a BA or a college diploma - a real one - without almost seeing a human in person. These initial studies had to look at usability, user interface and digital literacy. They had to research even cognitive measures, how the mind pays attention to a screen, visual studies on effects on the eyes, even worries about the health effects of Wi-Fi wireless transmissions. Anyway, eLearning has made it's mark, and it is going to stick around for a long time.

I have been practicing meditation for many years so I knew about MBSR and the research that has been developed on meditation in neuroscience and medicine. There have been research studies on the effectiveness of meditation not only from Jon Kabat-Zinn, founder of MBSR, but also from Herbert Benson, Richard Davidson, and so many others. I knew that the Buddhist monk Matthieu Ricard (in picture here at left) was in Davidson's fMRI and EEG studies on compassion and the meditating brain.  Just yesterday a new article on the benefits of MBSR and Tai Chi exercise for healing those surviving from breast cancer appeared on the Kurzweil Accelerating Intelligence website.  Cheng Man-ch'ing is smiling and proven right again, as Tai Chi really helped helped him recover from illness.

I have admired the work Jon Kabat-Zinn for many years, though I had never studied his works - until now. I am e-Learning my way through a free online 8 week course based on MBSR, about how it was developed and delivered, as well as the benefits for health that the research has shown.  Before I only knew about the benefits his teachings were having on those in palliative care or who were diagnosed with chronic illness - the meditation as healing medicine model - stress is the silent killer.  I also liked the secular, or one might say, the scientific approach. Now that I have been taking the MBSR course, I really have no qualms about doing so without a human for guidance. This is mostly due to my own experience and learning from meditation teachers, going on retreats, reading, and doing daily practice. I have also studied Buddhism in India, Nepal and Korea. Can't really say that I ever learned meditation before through an online interface. Call me misguided if you will, but I trust my instincts. Well, I did learn Vipassana in a semi-remote sort of way.

Many of the basic techniques in MBSR come from a meditation practice called Vipassana, or insight meditation. The main focus is on watching the breath or mindful awareness of breathing, called Anapanasati in Sanskrit. I did an 11 day Vipassana retreat in Massachusetts taught by S. N. Goenka from Burma. He was not there, but he may as well have been, because they used videos and tapes in the meditation hall to present the instructions. He has many other centres around the world. I thought it was very effective, even though my previous experience with meditation teaching was  learning discipline by sitting at the feet of the masters. This is the main reason why I feel confident in doing an 8 week online MBSR course. Another reason is that the course is exceptionally well designed with guided meditations, readings, video instructions, research articles, teachers with lots of experience- the whole works.  I will provide the link to The MBSR online course that I am following at the end of this post. The online course I am taking is free, but I have looked around and seen some that are not. That 11 day Vipassana course I took in Massachusetts, which including a place to sleep and food, was also free. You give "dana" according to what you think you can.

Generally speaking I would always advise studying with a human presence for a traditional discipline that has been past down for generations, if not millennium. The Tibetan people call the Dali Lama "Kundun", which means "The Presence". Call me a conservative in this respect, but there are just too many subtle things that can go wrong without the guidance of a teacher. On the other hand, I am very, very impressed with the secular or scientific approach of Kabat-Zinn in the design and delivery of the MBSR course.  It would be great however to take the course from him or some of his qualified fellow instructors in person, and I have looked around and there centers and courses locally where it is taught. It is all over the map now.

One criticism I have is learning some basic yoga exercises online, which is one part of the overall MBSR program. Listening or watching videos of yoga postures, and trying to follow along, creates risks of injury, for practitioners of any age. Injury can happen even in a center where a teacher is present, but the presence of the teacher is more reassuring. Learning dynamic movements or mental training is not like reading a book; it is immersive, interactive and interpersonal.  When I was trying to learn Tai Chi Ch'uan from the Cheng Man-ch'ing book by looking in a mirror, I developed aches and pains from unusual twisting of my body. Something similar is happening as I am lying on the floor receiving audio instructions on yoga postures. OK, maybe blame myself for not being careful.  I heard once that physiotherapists are getting a lot of business from people who are just taking up yoga. There are a lot of not so qualified instructors out there. To be fair, there may also be a lot of people who may not have realistic expectations about how to train properly and do not know their limits.

In fact after I took the MBSR online course and kindly received my certificate, Dave Potter changed the yoga links to emphasis watching the videos over listening to the audio. Hopefully this will make remote learning easier for people, who may not have the added benefit of prior experience doing yoga or having an instructor or someone with experience for guidance.

The online MBSR course I am taking is here: